Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate CCNA_03657 CCNA_03657 tryptophan synthase alpha chain
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__Caulo:CCNA_03657 Length = 275 Score = 239 bits (611), Expect = 3e-68 Identities = 128/249 (51%), Positives = 161/249 (64%), Gaps = 7/249 (2%) Query: 3 RIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADGP 62 RIDRRFAALKA NR G + +V AGDP ++++ L AGADLIELG PFSDPMA+GP Sbjct: 5 RIDRRFAALKAENRAGFVTYVMAGDPDAATTLSVLKGLPAAGADLIELGFPFSDPMAEGP 64 Query: 63 VIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQAG 122 IQ A++R + G+ L L VAAFR+ D DTPI+LMGYLNP+ G+ FA A +AG Sbjct: 65 TIQRAAQRGLKSGMTLQGTLDLVAAFREGDQDTPIILMGYLNPVLNKGFETFAALAAKAG 124 Query: 123 VDGVLLVDCPLEESAVLQPLRDA----GLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSF 178 VDG+++VDCP EE+ PL DA G+ I LAAPTT+ +R+ + GF+YYVS Sbjct: 125 VDGLIIVDCPPEEA---DPLSDALEAEGIALIRLAAPTTDDARLPMVVRRTSGFVYYVSV 181 Query: 179 AGITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDR 238 AG+TG D+A V +R + PVAVGFGIR A A+A ADA V+GSALVD Sbjct: 182 AGVTGVKSADAADVAPAVERLRKASGLPVAVGFGIRTPDQAAAVAKVADAAVVGSALVDE 241 Query: 239 LAGATDAGE 247 + A E Sbjct: 242 IESAAQLNE 250 Lambda K H 0.322 0.136 0.394 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 242 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 266 Length of database: 275 Length adjustment: 25 Effective length of query: 241 Effective length of database: 250 Effective search space: 60250 Effective search space used: 60250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate CCNA_03657 CCNA_03657 (tryptophan synthase alpha chain)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha subunit (EC 4.2.1.20))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00262.hmm # target sequence database: /tmp/gapView.18372.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00262 [M=256] Accession: TIGR00262 Description: trpA: tryptophan synthase, alpha subunit Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-79 253.0 0.1 1.2e-79 252.8 0.1 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_03657 CCNA_03657 tryptophan synthase a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_03657 CCNA_03657 tryptophan synthase alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 252.8 0.1 1.2e-79 1.2e-79 1 248 [. 10 256 .. 10 268 .. 0.96 Alignments for each domain: == domain 1 score: 252.8 bits; conditional E-value: 1.2e-79 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvek 73 f++lk+++ fv++v agdPd++++l ++k l aGad++ElG+pfsDP+a+Gptiq+a++R lk+g++++ lcl|FitnessBrowser__Caulo:CCNA_03657 10 FAALKAENRAGFVTYVMAGDPDAATTLSVLKGLPAAGADLIELGFPFSDPMAEGPTIQRAAQRGLKSGMTLQG 82 788999******************************************************************* PP TIGR00262 74 alellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqifl 146 +l+l++++re ++ Pi+l+ y n++++kg e+F a a++agvdg++++D P eead l +a + +g++ i l lcl|FitnessBrowser__Caulo:CCNA_03657 83 TLDLVAAFREGDQDTPIILMGYLNPVLNKGFETFAALAAKAGVDGLIIVDCPPEEADPLSDALEAEGIALIRL 155 ************************************************************************* PP TIGR00262 147 vaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkel 219 +aPt+++ rl + ++++GfvY vsvaGvtg+++ +++v +++++++ s Pv+vGFGi ++q+ ++ ++ lcl|FitnessBrowser__Caulo:CCNA_03657 156 AAPTTDDARLPMVVRRTSGFVYYVSVAGVTGVKSADAADVAPAVERLRKASGLPVAVGFGIRTPDQAAAVAKV 228 ************************************************************************9 PP TIGR00262 220 gadgvivGsAlvkiieeklddeekaleel 248 ad+++vGsAlv+ ie + +e+++e++ lcl|FitnessBrowser__Caulo:CCNA_03657 229 -ADAAVVGSALVDEIESAAQLNENVTEKV 256 .889************9988666665554 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (275 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.53 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory